This paper aims to apply the national innovation system(NIS) perspective to developing countries. Although the NIS perspective has been influential not only in academic research but also in government policy-making, it has not been very successful in identifying innovation systems of developing countries, since the concept was thought only appropriate for evaluating those of developed countries. In this research, the difficulties of applying the NIS perspective to developing countries and the possibility of an alternative framework are discussed. A comparative study for identifying NSIs of developing countries follows. To reveal the contrasting characteristics for identifying national innovation systems, different levels of NIS formation in five countries – Cambodia, Lao PDR, Myanmar, Thailand and Vietnam – in the Greater Mekong Subregion are presented by comparing with that of Malaysia. This work may be found useful in carrying out international development aid in the area of science and technology policy.